During application process to a graduate school in the US, I was asked to submit transcripts from all schools I attended. At the time of application, I was recently accepted to another unknown (by many-many orders of magnitude less known than the program I am applying to) PhD program in my home country. I was not given a transcript from this school, because at the time of application I was enrolled for only two months, and was not taking courses, so I did not upload a transcript on their site. I mentioned that I will be working at the school in my SoP, but never underlined in my application that it will be doctoral studies. When I was invited for an interview, I forwarded on my CV where I mentioned that I was a PhD student at the school. Now I've been accepted to the new school. I may be worrying too much, but could there be any problems in the future because I did not upload much info about that school in my online application? What should I do (if anything) in my case?
It sounds that you knowingly, and intentionally, deceived the school you were applying to by mentioning that you were working at a university, but leaving out that you were a PhD student in your statement of purpose. The fact that you mentioned that you were currently a PhD student during your interview makes the behavior a little less atrocious. That said, I have never heard of a graduate program punishing a student for omitting information from their statement of purpose.
As far as the transcripts are concerned,
at the time of application I was enrolled for only two months, and was not taking courses, so I did not upload a transcript on their site.
again, you were not fully honest, but it is not obvious to me that all universities can generate a transcript for a student during their first semester when they are not taking any classes.
Again, nothing bad is likely to come of your behavior, that said, in the future, you should just be honest and forth coming about your situation.